Thank you, Randy. Now it's clear. Maia Randy Read wrote:
Hi Maia,
The "copies" keyword is a shorthand for convenience in the common case that both your model and the sequence refer to a monomer, and what it does is set two separate keywords, copies_to_find and component_copies, to the same value. If you want to set these separately (e.g. you're searching for one copy of a dimer but your sequence is for the monomer), then you should be able to say "copies_to_find=1 component_copies=2".
Regards,
Randy
On 12 Sep 2009, at 01:56, Maia Cherney wrote:
Hi Tom, thank you for your reply. Still, the first question remains, if a model has two identical copies, but the sequence is for a monomer, what number of copies should I use: of model or of monomers?
Maia
Thomas C. Terwilliger wrote:
Hi Maia,
This is the example from the website:
Run AutoMR using coords.pdb as search model, native.sca as data, assume RMS between coords.pdb and true model is about 0.85 A, the sequence of true model is seq.dat and there is 1 copy in the unit cell:
phenix.automr coords.pdb native.sca RMS=0.85 seq.dat copies=1 \ n_cycle_rebuild_max=2 n_cycle_build_max=2
1. 1 copy of what: model.pdb or seq.dat? Model.pdb could be a dimer and seq.dat a monomer.
In this example we are assuming that model.pdb is a monomer and seq.dat is the sequence of that monomer.
2. 1 copy in the unit cell. Is it really in the unit cell? Usually we use number of copies in the asymmetric unit.
That one is a very bad typo. Yes, I meant one in the asymmetric unit. I have just fixed that in the documentation...
All the best, Tom T
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb